Cryptic Transmission of Novel Coronavirus Revealed by Genomic Epidemiology

“The field of genomic epidemiology focuses on using the genetic sequences of pathogens to understand patterns of transmission and spread. Viruses mutate very quickly and accumulate changes during the process of transmission from one infected individual to another. The novel coronavirus which is responsible for the emerging COVID-19 pandemic mutates at an average of about two mutations per month. After someone is exposed they will generally incubate the virus for ~5 days before symptoms develop and transmission occurs…

…We believe this may have occurred by the WA1 case having exposed someone else to the virus in the period between Jan 15 and Jan 19 before they were isolated. If this second case was mild or asymptomatic, contact tracing efforts by public health would have had difficulty detecting it. After this point, community spread occurred and was undetected due to the CDC narrow case definition that required direct travel to China or direct contact with a known case to even be considered for testing. This lack of testing was a critical error and allowed an outbreak in Snohomish County and surroundings to grow to a sizable problem before it was even detected.

Knowing that transmission was initiated on Jan 15 allows us to estimate the total number of infections that exist in this cluster today. Our preliminary analysis puts this at 570 with an 90% uncertainty interval of between 80 and 1500 infections

…We know that Wuhan went from an index case in ~Nov-Dec 2019 to several thousand cases by mid-Jan 2020, thus going from initial seeding event to widespread local transmission in the span of ~9-10 weeks. We now believe that the Seattle area seeding event was ~Jan 15 and we’re now ~7 weeks later. I expect Seattle now to look like Wuhan around ~1 Jan, when they were reporting the first clusters of patients with unexplained viral pneumonia. We are currently estimating ~600 infections in Seattle, this matches my phylodynamic estimate of the number of infections in Wuhan on Jan 1.”

Trevor Bedford, “Cryptic transmission of novel coronavirus revealed by genomic epidemiology.” Bedford Lab. March 2, 2020.

Roughly speaking, the take-away from this article is that 9-10 weeks after you have cases in your area, you should expect widespread transmission. The article outlines things you can do to minimize your risk of exposure:

  • Practicing social distancing, such as limiting attendance at events with large groups of people
  • Working from home, if your job and employer allows it
  • Staying home if you are feeling ill
  • Take your temperature daily, if you develop a fever, self-isolate and call your doctor
  • Implementing good hand washing practices – it is extremely important to wash hands regularly
  • Covering coughs and sneezes in your elbow or tissue
  • Avoiding touching your eyes, nose, and mouth with unwashed hands
  • Disinfecting frequently touched surfaces, such as doorknobs
  • Beginning some preparations in anticipation of social distancing or supply chain shortages, such as ensuring you have sufficient supplies of prescription medicines and ensuring you have about a 2 week supply of food and other necessary household goods.
  • With these preparation in mind, it is important to not panic buy. Panic buying unnecessarily increases strain on supply chains and can make it difficult to ensure that everyone is able to get supplies that they need.